Unfortunately for both Peter and his native Italy, during the height of the Inquisition, his knowledge of physics and philosophy was mistaken for witchcraft and magic, and he was incarcerated, and placed on trial. His captors charged him with false accusations, and made wild and unfounded claims about his practises and personal beliefs; mainly that with the aid of the devil, he recovered all the money he paid away, and that he possessed a philosopher's stone, which he used as the source of all his knowledge.

It was highly likely that he would have been found guilty of his non-existent crimes and burnt alive, had he survived his trial. In 1316 he died, aged sixty-six, alone in his cell. His apologists moved his body from location to location to save it from being burnt by his witch hunter captors. Its final resting place is St. Augustin's Church, where he was finally buried without a marker or epitaph.